NMR paper Structural and dynamic studies of DNA recognition by NF-?B p50 RHR homodimer using methyl NMR spectroscopy

		BioNMR > Educational resources > Journal club
[NMR paper] Structural and dynamic studies of DNA recognition by NF-?B p50 RHR homodimer using methyl NMR spectroscopy

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

06-24-2022, 11:45 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,185

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Structural and dynamic studies of DNA recognition by NF-?B p50 RHR homodimer using methyl NMR spectroscopy

Structural and dynamic studies of DNA recognition by NF-?B p50 RHR homodimer using methyl NMR spectroscopy

Protein dynamics involving higher-energy sparsely populated conformational substates are frequently critical for protein function. This study describes the dynamics of the homodimer (p50)2 of the p50 Rel homology region (RHR) of the transcription factor NF-?B, using 13C relaxation dispersion experiments with specifically (13C, 1H)-labeled methyl groups of Ile (?), Leu and Val. Free (p50)2 is highly dynamic in solution, showing ?s-ms relaxation dispersion consistent with exchange between the...

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
NMR: an essential structural tool for integrative studies of T cell development, pMHC ligand recognition and TCR mechanobiology NMR: an essential structural tool for integrative studies of T cell development, pMHC ligand recognition and TCR mechanobiology Abstract Early studies of T cell structural biology using X-ray crystallography, surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) focused on a picture of the Î±Î²T cell receptor (Î±Î²TCR) component domains and their cognate ligands (peptides bound to MHC molecules, i.e. pMHCs) as static interaction partners. Moving forward requires integrating this corpus of data with dynamic technologies such as...	nmrlearner	Journal club	0	03-24-2019 10:41 PM
[ASAP] Methyl-Based NMR Spectroscopy Methods for Uncovering Structural Dynamics in Large Proteins and Protein Complexes Methyl-Based NMR Spectroscopy Methods for Uncovering Structural Dynamics in Large Proteins and Protein Complexes https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.8b00953/20181026/images/medium/bi-2018-00953s_0006.gif Biochemistry DOI: 10.1021/acs.biochem.8b00953 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/VOv8DrY-3do More...	nmrlearner	Journal club	0	11-25-2018 06:02 AM
Measuring the signs of the methyl 1 H chemical shift differences between major and â??invisibleâ?? minor protein conformational states using methyl 1 H multi-quantum spectroscopy Measuring the signs of the methyl 1 H chemical shift differences between major and â??invisibleâ?? minor protein conformational states using methyl 1 H multi-quantum spectroscopy Abstract Carrâ??Purcellâ??Meiboomâ??Gill (CPMG) type relaxation dispersion experiments are now routinely used to characterise protein conformational dynamics that occurs on the Î¼s to millisecond (ms) timescale between a visible major state and â??invisibleâ?? minor states. The exchange rate(s) ( \( k_{{{\text{ex}}}} \) ...	nmrlearner	Journal club	0	03-21-2018 04:04 PM
[NMR paper] Chiral Recognition Studies of ?-(Nonafluoro-tert-butoxy)carboxylic Acids by NMR Spectroscopy. Chiral Recognition Studies of ?-(Nonafluoro-tert-butoxy)carboxylic Acids by NMR Spectroscopy. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Chiral Recognition Studies of ?-(Nonafluoro-tert-butoxy)carboxylic Acids by NMR Spectroscopy. J Org Chem. 2015 Jun 19;80(12):6267-74 Authors: Nemes A, Csóka T, Béni S, Farkas V, Rábai J, Szabó D Abstract Three chiral ?-(nonafluoro-tert-butoxy)carboxylic acids (R)-1, (RS)-2, (R)-3 were synthesized to examine...	nmrlearner	Journal club	0	03-15-2016 11:57 AM
[NMR paper] Just a Flexible Linker? The Structural and Dynamic Properties of CBP-ID4 Revealed by NMR Spectroscopy. Just a Flexible Linker? The Structural and Dynamic Properties of CBP-ID4 Revealed by NMR Spectroscopy. Just a Flexible Linker? The Structural and Dynamic Properties of CBP-ID4 Revealed by NMR Spectroscopy. Biophys J. 2016 Jan 19;110(2):372-381 Authors: Piai A, Calçada EO, Tarenzi T, Grande AD, Varadi M, Tompa P, Felli IC, Pierattelli R Abstract Here, we present a structural and dynamic description of CBP-ID4 at atomic resolution. ID4 is the fourth intrinsically disordered linker of CREB-binding protein (CBP). In spite of the...	nmrlearner	Journal club	0	01-21-2016 01:08 PM
3D-TROSY-based backbone and ILV-methyl resonance assignments of a 319-residue homodimer from a single protein sample 3D-TROSY-based backbone and ILV-methyl resonance assignments of a 319-residue homodimer from a single protein sample Abstract The feasibility of practically complete backbone and ILV methyl chemical shift assignments from a single -labeled protein sample of the truncated form of ligand-free Bst-Tyrosyl tRNA Synthetase (Bst-Î?YRS), a 319-residue predominantly helical homodimer, is established. Protonation of ILV residues at methyl positions does not appreciably detract from the quality of TROSY triple resonance data. The assignments are performed at 40 Â°C to improve the sensitivity of...	nmrlearner	Journal club	0	09-10-2012 01:48 AM
Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methylâ??methyl nuclear overhauser enhancement spectroscopy Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methylâ??methyl nuclear overhauser enhancement spectroscopy Abstract Methyl-transverse relaxation optimized spectroscopy is rapidly becoming the preferred NMR technique for probing structure and dynamics of very large proteins up to ~1 MDa in molecular size. Data interpretation, however, necessitates assignment of methyl groups which still presents a very challenging and time-consuming process. Here we demonstrate that, in combination with a known 3D structure, paramagnetic...	nmrlearner	Journal club	0	09-26-2011 06:42 AM
[NMR paper] Conformational studies of microcystin-LR using NMR spectroscopy and molecular dynamic Conformational studies of microcystin-LR using NMR spectroscopy and molecular dynamics calculations. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Conformational studies of microcystin-LR using NMR spectroscopy and molecular dynamics calculations. Biochemistry. 1996 Mar 12;35(10):3197-205 Authors: Trogen GB, Annila A, Eriksson J, Kontteli M, Meriluoto J, Sethson I, Zdunek J, Edlund U NMR spectroscopy in aqueous and dimethyl sulfoxide/water solutions is used to determine the...	nmrlearner	Journal club	0	08-22-2010 02:27 PM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off